Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/WrappPlotRepartition.py @ 1:30c5431d8ce4

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
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2 from optparse import OptionParser
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3 import tarfile
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 import re
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 import shutil
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 import subprocess
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9 SMART_PATH = "%sSMART" % os.environ["REPET_PATH"]
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 def toTar(tarFileName, directory):
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12 fileName = os.path.splitext(tarFileName)[0]
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13 fileNameBaseName = os.path.basename(fileName)
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14 tfile = tarfile.open(fileName + ".tmp.tar", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 list = os.listdir(directory)
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16 for file in list:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 if re.search(str(fileNameBaseName), file):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 tfile.add(file)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 tfile.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 if __name__ == "__main__":
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25 magnifyingFactor = 1000
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27 # parse command line
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28 description = "Plot the repartition of different data on a whole genome. (This tool uses 1 input file only, the different values being stored in the tags. See documentation to know more about it.) [Category: Visualization]"
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31 parser = OptionParser(description = description)
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32 parser.add_option("-i", "--input",dest="inputFileName",action="store",type="string",help="input file name [compulsory] [format: file in GFF3 format]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 parser.add_option("-n", "--names",dest="names", action="store", type="string", help="name for the tags (separated by commas and no space) [compulsory] [format: string]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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34 parser.add_option("-o", "--output",dest="outTarFileName",action="store",type="string", help="output file [compulsory] [format: output file tar format]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 parser.add_option("-c", "--color",dest="colors",action="store",default=None,type="string", help="color of the lines (separated by commas and no space) [format: string]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 parser.add_option("-f", "--format",dest="format",action="store",default="png",type="string", help="format of the output file [format: string] [default: png]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 parser.add_option("-r", "--normalize",dest="normalize",action="store_true", default=False,help="normalize data (when panels are different) [format: bool] [default: false]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 parser.add_option("-l", "--log",dest="log",action="store",default="",type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]")
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40 (options, args) = parser.parse_args()
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42
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43 absPath = os.getcwd()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 print "the current path is :", absPath
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 directory = "/tmp/wrappPlotRepartition"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 print "the dir path is :", directory
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47 if not os.path.exists(directory):
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48 os.makedirs(directory)
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49 os.chdir(directory)
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50 if options.inputFileName != None and options.format != None and options.outTarFileName != None:
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51 outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
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52 cmd = "python %s/Java/Python/plotRepartition.py -i %s -o %s -D %s" % (SMART_PATH, options.inputFileName, outputFileName, directory)
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53 if options.names != None :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 cmd += " -n %s" % options.names
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 else: print "You must choose tag names !"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 if options.colors != None :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 cmd += " -c %s" % options.colors
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 if options.format != None:
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59 cmd += " -f %s" % options.format
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60 if options.normalize :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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61 cmd += " -r "
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62 if options.log != "" :
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63 cmd += " -l %s" % options.log
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64
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65 print "cmd is: ", cmd
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66 status = subprocess.call(cmd, shell=True)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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67 if status != 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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68 raise Exception("Problem with the execution of command!")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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69 toTar(options.outTarFileName, directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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70 shutil.rmtree(directory)
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71